Mercurial > repos > immport-devteam > flowtext_scatterplot
comparison getDensityPlots_text.xml @ 1:754d511df1a3 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9"
author | azomics |
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date | Tue, 14 Jul 2020 09:40:13 -0400 |
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0:cc2266d3e611 | 1:754d511df1a3 |
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1 <tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.1+galaxy0" profile="18.01"> | |
2 <description>for any given markers in a txt-converted FCS file</description> | |
3 <requirements> | |
4 <requirement type="package" version="3.3.2">r-ggplot2</requirement> | |
5 <requirement type="package" version="2.23_17">r-kernsmooth</requirement> | |
6 </requirements> | |
7 <stdio> | |
8 <exit_code range="1:9" level="fatal" /> | |
9 <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" /> | |
10 <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" /> | |
11 <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" /> | |
12 <exit_code range="13:" level="fatal"/> | |
13 </stdio> | |
14 <command><![CDATA[ | |
15 Rscript $__tool_directory__/getDensityPlots_text.R '${input}' '${channels}' '${output}' '${outformat}' | |
16 ]]> | |
17 </command> | |
18 <inputs> | |
19 <param format="flowtext" name="input" type="data" label="txt-converted FCS file"/> | |
20 <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/> | |
21 <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load."> | |
22 <option value="PNG">PNG</option> | |
23 <option value="PDF">PDF</option> | |
24 </param> | |
25 </inputs> | |
26 <outputs> | |
27 <data format="png" name="output" label="Scatter Plots of ${channels} from ${input.name} in ${outformat}"> | |
28 <change_format> | |
29 <when input="outformat" value="PDF" format="pdf" /> | |
30 </change_format> | |
31 </data> | |
32 </outputs> | |
33 <tests> | |
34 <test> | |
35 <param name="input" value="input.flowtext"/> | |
36 <param name="channels" value="i.e.:1,3,4"/> | |
37 <param name="outformat" value="PDF"/> | |
38 <output name="output" file="graph.pdf" compare="sim_size" delta="2000000"/> | |
39 </test> | |
40 <test> | |
41 <param name="input" value="input.flowtext"/> | |
42 <param name="channels" value="1,3,5"/> | |
43 <param name="outformat" value="PNG"/> | |
44 <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/> | |
45 </test> | |
46 </tests> | |
47 <help><![CDATA[ | |
48 This tool allows generation of density scatter plots using ggplot2. | |
49 | |
50 ----- | |
51 | |
52 **Input files** | |
53 | |
54 This tool takes txt-converted FCS files as input. | |
55 | |
56 **Output files** | |
57 | |
58 This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated. | |
59 | |
60 class:: warningmark | |
61 | |
62 PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally. | |
63 | |
64 ----- | |
65 | |
66 **Example** | |
67 | |
68 *Output*: | |
69 | |
70 .. image:: ./static/images/flowtools/flowtextgraph.png | |
71 ]]> | |
72 </help> | |
73 <citations> | |
74 <citation type="bibtex">@BOOK{, | |
75 author = {Hadley Wickham}, | |
76 title = {ggplot2: Elegant Graphics for Data Analysis}, | |
77 publisher = {Springer-Verlag New York}, | |
78 year = {2009}, | |
79 isbn = {978-0-387-98140-6}, | |
80 url = {http://ggplot2.org}, | |
81 }</citation> | |
82 </citations> | |
83 </tool> |